The manipulation of the antiferromagnetic interlayer coupling in epitaxial Fe/Cr/Fe(001) trilayers by 5 keV He ion beam irradiation has been investigated. It is shown that even for irradiation with low fluences a drastic change in strength of the coupling appears. For thin Cr spacers (below 0.6-0.7 nm) it decreases with fluence, becoming ferromagnetic for fluences above 2x10(14) ions/cm(2). The effect is connected with the creation of magnetic bridges in the layered system due to atomic exchange events caused by the bombardment. For thicker Cr spacers an enhancement of the antiferromagnetic coupling strength is found. A possible explanation of the enhancement effect is given.